8BD3

Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	1, 7	Chlorophyll a-b binding protein, chloroplastic	polymer	214	23060.1	2	UniProt (A0A2P6TPU9) Pfam (PF00504) In PDB	Chlorella ohadii
2	2, 4, G, 9, q...	Chlorophyll a-b binding protein, chloroplastic	polymer	222	23850.7	6	UniProt (A0A2P6TDA6) Pfam (PF00504) In PDB	Chlorella ohadii
3	3, 5, N, 8, p...	Chlorophyll a-b binding of LHCII	polymer	221	23847.9	6		Chlorella ohadii
4	6, 0	Chlorophyll a-b binding of LHCII	polymer	217	23455.5	2		Chlorella ohadii
5	A, a	Photosystem II protein D1	polymer	336	37230.3	2	UniProt (W8SIR2) Pfam (PF00124) In PDB	Chlorella ohadii
6	B, b	Photosystem II CP47 reaction center protein	polymer	504	55754.3	2	UniProt (W8TIK4) Pfam (PF00421) In PDB	Chlorella ohadii
7	C, c	Photosystem II CP43 reaction center protein	polymer	448	49161.1	2	UniProt (A0A076EAP1) Pfam (PF00421) In PDB	Chlorella ohadii	PSII 43 kDa protein,Protein CP-43
8	D, d	Photosystem II D2 protein	polymer	342	38459.9	2	UniProt (W8SYD4) Pfam (PF00124) In PDB	Chlorella ohadii
9	E, e	Cytochrome b559 subunit alpha	polymer	81	9204.3	2	UniProt (W8SU91) Pfam (PF00283) Pfam (PF00284) In PDB	Chlorella ohadii	PSII reaction center subunit V
10	F, f	Cytochrome b559 subunit beta	polymer	37	4262.1	2	UniProt (P56310) Pfam (PF00283) In PDB	Chlorella ohadii	PSII reaction center subunit VI
11	H, h	Photosystem II reaction center protein H	polymer	67	7223.4	2	UniProt (W8SIT0) Pfam (PF00737) In PDB	Chlorella ohadii
12	I, i	Photosystem II reaction center protein I	polymer	34	3871.5	2	UniProt (A0A5P4ND48) Pfam (PF02532) In PDB	Chlorella ohadii	PSII-I,PSII 4.8 kDa protein
13	J, j	Photosystem II reaction center protein J	polymer	38	3813.5	2	UniProt (W8TIH6) Pfam (PF01788) In PDB	Chlorella ohadii
14	K, k	Photosystem II reaction center protein K	polymer	37	4140.0	2	UniProt (P56348) Pfam (PF02533) In PDB	Chlorella ohadii	PSII-K
15	L, l	Photosystem II reaction center protein L	polymer	37	4260.0	2	UniProt (P56339) Pfam (PF02419) In PDB	Chlorella ohadii	PSII-L
16	M, m	Photosystem II reaction center protein M	polymer	57	5621.9	2	UniProt (A0A5P4NAV9) Pfam (PF05151) In PDB	Chlorella ohadii
17	O, o	Chloroplast oxygen-evolving enhancer protein 1	polymer	240	25449.5	2	UniProt (A0A5P4NF37) Pfam (PF01716) In PDB	Chlorella ohadii
18	R, r	Chlorophyll a b binding CP29	polymer	236	25803.7	2		Chlorella ohadii
19	S, s	Chlorophyll a b-binding CP26	polymer	257	27369.8	2		Chlorella ohadii
20	T, t	Photosystem II reaction center protein T	polymer	30	3476.2	2	UniProt (P56327) Pfam (PF01405) In PDB	Chlorella ohadii	PSII-T
21	V, v	Photosystem II reaction center protein Ycf12	polymer	32	3319.0	2	UniProt (A0A076EAR3) Pfam (PF05969) In PDB	Chlorella ohadii
22	W, w	Photosystem II reaction center W protein	polymer	60	6623.4	2		Chlorella ohadii
23	X, x	Photosystem II reaction center protein X	polymer	37	3526.0	2		Chlorella ohadii
24	Y, y	Multifunctional fusion protein	polymer	221	23864.0	2	UniProt (A0A2P6U5M3) Pfam (PF00504) In PDB	Chlorella ohadii
25	Z, z	Photosystem II reaction center protein Z	polymer	62	6727.1	2	UniProt (W8SKL0) Pfam (PF01737) In PDB	Chlorella ohadii
26	U, u	Chloroplast oxygen-evolving enhancer protein 3	polymer	144	15948.1	2	UniProt (A0A5P4NB29) Pfam (PF05757) In PDB	Chlorella ohadii
27	Q1, q1	Chloroplast PsbY	polymer	34	3697.3	2	UniProt (A0A5P4NEE0) In PDB	Chlorella ohadii
28	P1, p1	Chloroplast photosystem II 10 kDa protein	polymer	108	11657.3	2	UniProt (A0A5P4NAS4) Pfam (PF04725) In PDB	Chlorella ohadii
29	F1, f1	Photosystem II oxygen evolving enhancer 2	polymer	188	20416.8	2		Chlorella ohadii
30	5, N, 8, 9, 4...	CHLOROPHYLL B	non-polymer		907.5	122	Chemie (CHL)
31	1, 4, 6, C, D...	CHLOROPHYLL A	non-polymer		893.5	270	Chemie (CLA)
32	y, S, Y, 1, 6...	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		568.9	36	Chemie (LUT)
33	0, g, t, q, d...	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	44	Chemie (LHG)
34	2, A, 0, g, d...	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	86	Chemie (LMG)
35	9, 4, 2, g, G...	(3R)-beta,beta-caroten-3-ol	non-polymer		552.9	6	Chemie (RRX)
36	G, q, r, y, S...	(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL	non-polymer		600.9	22	Chemie (NEX)
37	q, g, G, R, 9...	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		600.9	8	Chemie (XAT)
38	G, 0, r, y, s...	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	24	Chemie (SQD)
39	a, A	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
40	a, A	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
41	a, A	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
42	a, A, d, D	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
43	t, v, D, h, z...	BETA-CAROTENE	non-polymer		536.9	22	Chemie (BCR)
44	d, D, a, A	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE	non-polymer		749.2	4	Chemie (PL9)
45	c, C	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD)
46	d, D	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
47	e, E	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
48	r, K, R, c	DODECYL-ALPHA-D-MALTOSIDE	non-polymer		510.6	4	Chemie (LMU)
49		water	water		18.0	224	Chemie (HOH)

Sequence modifications

1, 7: 39 - 252 (UniProt: A0A2P6TPU9)

PDB	External Database	Details
Leu 195	Phe 719	conflict
Glu 225	Asp 749	conflict
Asn 250	Thr 774	conflict

2, 4, G, 9, q, g: 40 - 261 (UniProt: A0A2P6TDA6)

PDB	External Database	Details
Thr 74	Ser 64	conflict

M, m: -24 - 0 (PDB: 8BD3)
M, m: 1 - 32 (UniProt: A0A5P4NAV9)

Contents of the asymmetric unit

Polymers	Number of chains	66
	Total formula weight	1180984.5
Non-Polymers*	Number of molecules	672
	Total formula weight	542583.2
All*	Total formula weight	1723567.7

*Water molecules are not included.